2 Program

The course takes place daily from 9am – 5pm (CEST), including coffee, lunch, and short breaks. Most of the time will be dedicated to practical exercises, complemented by lectures and demos.

We expect that participants will prepare for the course in advance. Instructions will be sent to the registered participants. Online support will be available.

The material follows open online book created by the course teachers, Orchestrating Microbiome Analysis, which supports R/Bioconductor framework for multi-omic data integration and analysis.

ML4microbiome

Figure source: Moreno-Indias et al. (2021) Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions. Frontiers in Microbiology 12:11.

2.1 Day 1 - Open data science

Reproducible workflows with R/Bioconductor and Quarto

Morning

9-10 Coffee, Welcome & Practicalities

10-11 Lecture: open & reproducible workflows

11-12 Introduction to CSC RStudio notebook

12-13 Lunch break

Afternoon

13-14 Reproducible reporting with Quarto

14-16 Working with data containers and workflows

2.2 Day 2 - Tabular data analysis

Morning

9-10 Lecture: analysis & visualization of tabular data (single omics)

10-12 Subsetting, transformations, and data summaries

12-13 Lunch break

Afternoon

13-14 Univariate data analysis and visualization

14-16 Multivariate data analysis and visualization

Evening

Informal course dinner (at own cost)

2.3 Day 3 - Multi-assay data integration

Morning

9-10 Lecture: analysis & visualization of multi-assay data (multi-omics)

10-12 Multi-assay data analysis and visualization

12-13 Lunch break

Afternoon

13-15: Q & A and advanced techniques (e.g. time series, machine learning, simulation)

15-16: Summary and wrap-up